scicom 0.2.0-java

data/test/test_sequence.rb

@@ -0,0 +1,63 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'env'
+require 'scicom'
+
+class SciComTest < Test::Unit::TestCase
+
+  context "R environment" do
+
+    #======================================================================================
+    #
+    #======================================================================================
+
+    setup do 
+
+      # creating a new instance of Renjin
+      @r1 = R.new
+
+    end
+
+    #======================================================================================
+    #
+    #======================================================================================
+
+    should "create an int sequence" do
+      
+      seq = R.seq(2, 10)
+
+      res = R.eval <<EOF
+      print(#{seq.r});
+      print(#{seq.r});
+print(ls());
+
+EOF
+
+    end
+
+  end
+
+end

data/test/test_subsetting.rb

@@ -0,0 +1,67 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'env'
+require 'scicom'
+
+class SciComTest < Test::Unit::TestCase
+
+  context "R Vectors" do
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    setup do 
+
+    end
+
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "slice a vector in multiple ways" do
+
+      vec = R.c(1, 2, 3, 4)
+
+      # access a given vector index
+      assert_equal(3, vec[3].gz)
+
+      # Method .gt gets the thruth value of the first element of the array
+      # Vector with negative index: all values are returned but the ones in the index
+      assert_equal(true, (R.c(1, 2, 4).eq vec[-3]).gt)
+
+      # New vector in the given range
+      assert_equal(true, (R.c(1, 2, 3).eq vec[(1..3)]).gt)
+
+      
+      vec[-(1..3)].pp
+
+    end
+
+  end
+
+end

data/test/test_tmp.rb

@@ -0,0 +1,67 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'env'
+require 'scicom'
+
+class SciComTest < Test::Unit::TestCase
+
+  context "R environment" do
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    setup do 
+
+      # create a list with named elements
+      @x = R.list(first: (1..10), second: R.c("yes","no"), third: R.c(TRUE,FALSE), 
+        fourth: R.gl(2,3))
+      
+      @seq = R.c((1..10))
+      @seq2 = R.c((1...10))
+      @str_vec = R.c("yes", "no")
+      @str_vec2 = R.c("yes", "yes")
+      @trth_vec = R.c(TRUE, FALSE)
+      @trth_vec2 = R.c(FALSE, FALSE)
+      @gl = R.gl(2, 3)
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "assign to a character vector" do
+
+      h = {f: :colnames, index: [[1]]}
+      p h[:f]
+      p h[:index]
+
+    end
+
+  end
+  
+end

data/test/test_vector.rb

@@ -0,0 +1,227 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'env'
+require 'scicom'
+
+class SciComTest < Test::Unit::TestCase
+
+  context "R Vectors" do
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    setup do 
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "create vectors of different types" do
+
+      # double vector
+      dbl_var = R.c(1, 2.5, 4.5)
+      assert_equal(2.5, dbl_var[2].gz)
+      assert_equal("double", dbl_var.typeof.gz)
+      assert_equal(3, dbl_var.length)
+      assert_equal(false, dbl_var.integer?)
+      assert_equal(true, dbl_var.double?)
+      assert_equal(true, dbl_var.numeric?)
+
+      # int vector: with the R.i, you get an integer rather than a double
+      int_var = R.c(R.i(1), R.i(6), R.i(10))
+      assert_equal("integer", int_var.typeof.gz)
+      assert_equal(3, int_var.length)
+      assert_equal(true, int_var.integer?)
+      
+      # logical vector: Use TRUE and FALSE to create logical vectors
+      log_var = R.c(TRUE, FALSE, TRUE, FALSE)
+      assert_equal("logical", log_var.typeof.gz)
+      assert_equal(4, log_var.length)
+      assert_equal(true, log_var.logical?)
+
+      # string vector: create string (character) vectors
+      chr_var = R.c("these are", "some strings")
+      assert_equal("character", chr_var.typeof.gz)
+      assert_equal(2, chr_var.length)
+      assert_equal(true, chr_var.character?)
+      assert_equal(true, chr_var.atomic?)
+      assert_equal(false, chr_var.numeric?)
+
+      # complex vector
+      comp_var = R.c(R.complex(real: 2, imaginary: 1), R.complex(real: 0, imaginary: 1))
+      assert_equal("complex", comp_var.typeof.gz)
+      assert_equal(2, comp_var.length)
+      assert_equal(false, comp_var.integer?)
+      assert_equal(false, comp_var.double?)
+      assert_equal(true, comp_var.complex?)
+      assert_equal(1, comp_var[2].im.gz)
+
+      ## create a complex normal vector
+      z = R.complex(real: R.rnorm(100), imaginary: R.rnorm(100))
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "create vectors with basic R functions" do
+
+      # R.c "flattens" the vectors
+      v1 = R.c(1, R.c(2, R.c(3, 4)))
+      assert_equal(true, (R.c(1, 2, 3, 4).eq v1).gt)
+
+      # R.rep repeats the given vector
+      vec2 = R.rep(R.c("A", "B", "C"), 3)
+      assert_equal(true, (R.c("A", "B", "C", "A", "B", "C", "A", "B", "C").eq vec2).gt)
+
+      # R.table calculates the frequencies of elements
+      vec3 = R.c("A", "B", "C", "A", "A", "A", "A", "B", "B")
+      table = R.table(vec3)
+      assert_equal(true, (R.c(R.i(5), R.i(3), R.i(1)) == table).gt)
+
+      # Ruby does not allow the ":" notation such as "1:3", this can be obtained
+      # by Ruby's range notation (1..3) or (1...3)
+      # does not include the last element
+      v2 = R.c((1...3))
+      assert_equal(true, (R.c(1, 2) == v2).gt)
+
+      # includes the last element
+      v3 = R.c((1..3))
+      assert_equal(true, (R.c(1, 2, 3) == v3).gt)
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "access vector elements" do
+
+      i1 = R.i(10)
+      # In R, and with SciCom vectors, indexing a vector returns a vector.  First index for 
+      # vector is 1 and not 0 as it is usual with Ruby, this is so, in order to be 
+      # consistent with R.
+      i3 = i1[1]
+      assert_equal(true, (i3 == i1).gt)
+
+      # double vector
+      dbl_var = R.c(1, 2.5, 4.5)
+      assert_equal(2.5, dbl_var[2].gz)
+      assert_equal(4.5, dbl_var[3].gz)
+
+      # indexing a vector outside of bound returns NA
+      assert_equal(NA, dbl_var[4].gz)
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "assign to a numeric vector" do
+
+      # assign to a given vector index
+      vec = R.c(1, 2, 3)
+      vec[1] = 0
+      assert_equal(true, (R.c(0, 2, 3) == vec).gt)
+
+      # assign to a vector slice
+      vec[R.c(1, 2)] = R.c(5, 6)
+      assert_equal(true, (R.c(5, 6, 3) == vec).gt)
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "assign to a character vector" do
+
+      vec = R.c("a", "b", "c")
+      vec[1] = "d"
+      assert_equal(true, (R.c("d", "b", "c").eq vec).gt)
+
+      # assign to a vector slice
+      vec[R.c(1, 2)] = R.c("e", "f")
+      assert_equal(true, (R.c("e", "f", "c").eq vec).gt)
+
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "match two vectors with %in%" do
+
+      vec1 = R.c(1, 2, 3, 4)
+      vec2 = R.c(1, 2, 3, 4)
+      vec3 = R.c(3, 4, 5)
+      vec4 = R.c(4, 5, 6, 7)
+
+      # R has functions defined with '%%' notation.  In order to access those functions
+      # from SciCom we use the '._' method with two arguments, the first argument is the
+      # name of the function, for instance, function %in%, the name of the method is ':in'
+      # Ex: vec1 %in% vec2 => vec1._ :in, vec2 
+      (vec1._ :in, vec2).pp
+      (vec1._ :in, vec3).pp
+      (vec2._ :in, vec4).pp
+      
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "Apply a Function over a List or Vector" do
+
+      x = R.list(a: (1..10), beta: R.exp(-3..3), logic: R.c(TRUE,FALSE,FALSE,TRUE))
+      x.pp
+      # compute the list mean for each list element
+      mean = R.lapply(x, "mean")
+      mean.pp
+
+      # median and quartiles for each list element
+      # quant = R.lapply(x, "quantile")
+      # quant = R.sapply(x, "quantile")
+      # quant.pp
+      # R.eval("x <- lapply(#{x.r}, quantile, c(0.25, 0.50, 0.75))")
+      # R.eval("print(x)")
+
+      # list of vectors
+      i39 = R.sapply((3..9), "seq")
+      i39.pp
+      sap = R.sapply(i39, "fivenum")
+      sap.pp
+
+    end
+
+  end
+
+end

data/version.rb

@@ -0,0 +1,2 @@
+$gem_name = "scicom"
+$version="0.2.0"

metadata

@@ -0,0 +1,196 @@
+--- !ruby/object:Gem::Specification
+name: scicom
+version: !ruby/object:Gem::Version
+  version: 0.2.0
+platform: java
+authors:
+- Rodrigo Botafogo
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2014-11-16 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: yard
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.8.5.2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 0.8.5.2
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: kramdown
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  prerelease: false
+  type: :development
+description: "SciCom (Scientific Computing) for Ruby brings the power of R to the\
+  \ Ruby community. SciCom \nis based on Renjin, a JVM-based interpreter for the R\
+  \ language for statistical computing.\n\nR on the JVM\n------------\n\nOver the\
+  \ past two decades, the R language for statistical computing has emerged as the\
+  \ de \nfacto standard for analysts, statisticians, and scientists. Today, a wide\
+  \ range of \nenterprises – from pharmaceuticals to insurance – depend on R for key\
+  \ business uses. Renjin \nis a new implementation of the R language and environment\
+  \ for the Java Virtual Machine (JVM),\nwhose goal is to enable transparent analysis\
+  \ of big data sets and seamless integration with \nother enterprise systems such\
+  \ as databases and application servers.\n\nRenjin is still under development, but\
+  \ it is already being used in production for a number \nof client projects, and\
+  \ supports most CRAN packages, including some with C/Fortran \ndependencies.\n\n\
+  SciCom and Renjin\n-----------------\n\nSciCom integrates with Renjin and allows\
+  \ the use of R inside a Ruby script. In a sense, \nSciCom is similar to other solutions\
+  \ such as RinRuby, Rpy2, PipeR, etc. However, since \nSciCom and Renjin both target\
+  \ the JVM there is no need to integrate both solutions and \nthere is no need to\
+  \ send data between Ruby and R, as it all resides in the same JVM. \nFurther, installation\
+  \ of SciCom does not require the installation of GNU R; Renjin is the \ninterpreter\
+  \ and comes with SciCom. Finally, although SciCom provides a basic interface to\
+  \ \nRenjin similar to RinRuby, a much tighter integration is also possible.\n"
+email: rodrigo.a.botafogo@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- Rakefile
+- version.rb
+- config.rb
+- lib/env.rb
+- lib/rinruby.rb
+- lib/scicom.rb
+- lib/JRubyR/list.rb
+- lib/JRubyR/vector.rb
+- lib/JRubyR/attributes.rb
+- lib/JRubyR/as_mdarray.rb
+- lib/JRubyR/logical_value.rb
+- lib/JRubyR/sequence.rb
+- lib/JRubyR/environment.rb
+- lib/JRubyR/list_orig.rb
+- lib/JRubyR/ruby_classes.rb
+- lib/JRubyR/function.rb
+- lib/JRubyR/index.rb
+- lib/JRubyR/rbsexp.rb
+- lib/JRubyR/renjin.rb
+- lib/JRubyR/dataframe.rb
+- test/env.rb
+- test/test_tmp.rb
+- test/test_attributes.rb
+- test/test_complete.rb
+- test/test_column-major.rb
+- test/test_double_assign.rb
+- test/test_double_receive.rb
+- test/test_distribution.rb
+- test/test_creation.rb
+- test/test_array.rb
+- test/test_sequence.rb
+- test/test_environment.rb
+- test/test_functions.rb
+- test/test_basic.rb
+- test/test_vector.rb
+- test/test_mdarray.rb
+- test/test_subsetting.rb
+- test/test_factor.rb
+- test/test_R_interface.rb
+- test/test_operators.rb
+- test/test_linear_model.rb
+- test/test_matrix.rb
+- test/test_dataframe.rb
+- test/test_list.rb
+- test/baseball.csv
+- doc/PypeR.pdf
+- doc/The R interface.docx
+- doc/Stat 133 Class Notes (Phil Spector).pdf
+- vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar
+- vendor/Renjin.pdf
+- target/helper.jar
+- README.md
+- README.md~
+- LICENSE.txt
+homepage: http://github.com/rbotafogo/scicom/wiki
+licenses:
+- GPL
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 2.1.9
+signing_key:
+specification_version: 4
+summary: Scientific Computing for Ruby
+test_files:
+- test/env.rb
+- test/test_tmp.rb
+- test/test_attributes.rb
+- test/test_complete.rb
+- test/test_column-major.rb
+- test/test_double_assign.rb
+- test/test_double_receive.rb
+- test/test_distribution.rb
+- test/test_creation.rb
+- test/test_array.rb
+- test/test_sequence.rb
+- test/test_environment.rb
+- test/test_functions.rb
+- test/test_basic.rb
+- test/test_vector.rb
+- test/test_mdarray.rb
+- test/test_subsetting.rb
+- test/test_factor.rb
+- test/test_R_interface.rb
+- test/test_operators.rb
+- test/test_linear_model.rb
+- test/test_matrix.rb
+- test/test_dataframe.rb
+- test/test_list.rb